2-Chloropyrimidine-5-boronic acid

Cat.NO.:A110557 Purity:98%

Product Details of [ 1003845-06-4 ]

CAS No. :	1003845-06-4
Formula :	C₄H₄BClN₂O₂
M.W :	158.35
SMILES Code :	ClC1=NC=C(C=N1)B(O)O
MDL No. :	MFCD08063113
InChI Key :	YTCIHPTZKKWKKC-UHFFFAOYSA-N
Pubchem ID :	21747362

Safety of [ 1003845-06-4 ]

GHS Pictogram:
Signal Word:	Warning
Hazard Statements:	H302-H315-H319-H332-H335
Precautionary Statements:	P261-P280-P305+P351+P338

Computational Chemistry of [ 1003845-06-4 ] Show Less

Physicochemical Properties

Num. heavy atoms	10
Num. arom. heavy atoms	6
Fraction Csp3	0.0
Num. rotatable bonds	1
Num. H-bond acceptors	4.0
Num. H-bond donors	2.0
Molar Refractivity	36.87
TPSA ? Topological Polar Surface Area: Calculated from Ertl P. et al. 2000 J. Med. Chem.	66.24 Å²

Lipophilicity

Log P_o/w (iLOGP)? iLOGP: in-house physics-based method implemented from Daina A et al. 2014 J. Chem. Inf. Model.	0.0
Log P_o/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by XLOGP program, version 3.2.2, courtesy of CCBG, Shanghai Institute of Organic Chemistry	0.07
Log P_o/w (WLOGP)? WLOGP: Atomistic method implemented from Wildman SA and Crippen GM. 1999 J. Chem. Inf. Model.	-1.19
Log P_o/w (MLOGP)? MLOGP: Topological method implemented from Moriguchi I. et al. 1992 Chem. Pharm. Bull. Moriguchi I. et al. 1994 Chem. Pharm. Bull. Lipinski PA. et al. 2001 Adv. Drug. Deliv. Rev.	-1.57
Log P_o/w (SILICOS-IT)? SILICOS-IT: Hybrid fragmental/topological method calculated by FILTER-IT program, version 1.0.2, courtesy of SILICOS-IT, http://www.silicos-it.com	-0.83
Consensus Log P_o/w? Consensus Log P_o/w: Average of all five predictions	-0.7

Water Solubility

Log S (ESOL):? ESOL: Topological method implemented from Delaney JS. 2004 J. Chem. Inf. Model.	-1.24
Solubility	9.03 mg/ml ; 0.057 mol/l
Class? Solubility class: Log S scale Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly	Very soluble
Log S (Ali)? Ali: Topological method implemented from Ali J. et al. 2012 J. Chem. Inf. Model.	-1.01
Solubility	15.3 mg/ml ; 0.0966 mol/l
Class? Solubility class: Log S scale Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly	Very soluble
Log S (SILICOS-IT)? SILICOS-IT: Fragmental method calculated by FILTER-IT program, version 1.0.2, courtesy of SILICOS-IT, http://www.silicos-it.com	-1.15
Solubility	11.3 mg/ml ; 0.0713 mol/l
Class? Solubility class: Log S scale Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly	Soluble

Pharmacokinetics

GI absorption? Gatrointestinal absorption: according to the white of the BOILED-Egg	High
BBB permeant? BBB permeation: according to the yolk of the BOILED-Egg	No
P-gp substrate? P-glycoprotein substrate: SVM model built on 1033 molecules (training set) and tested on 415 molecules (test set) 10-fold CV: ACC=0.72 / AUC=0.77 External: ACC=0.88 / AUC=0.94	No
CYP1A2 inhibitor? Cytochrome P450 1A2 inhibitor: SVM model built on 9145 molecules (training set) and tested on 3000 molecules (test set) 10-fold CV: ACC=0.83 / AUC=0.90 External: ACC=0.84 / AUC=0.91	No
CYP2C19 inhibitor? Cytochrome P450 2C19 inhibitor: SVM model built on 9272 molecules (training set) and tested on 3000 molecules (test set) 10-fold CV: ACC=0.80 / AUC=0.86 External: ACC=0.80 / AUC=0.87	No
CYP2C9 inhibitor? Cytochrome P450 2C9 inhibitor: SVM model built on 5940 molecules (training set) and tested on 2075 molecules (test set) 10-fold CV: ACC=0.78 / AUC=0.85 External: ACC=0.71 / AUC=0.81	No
CYP2D6 inhibitor? Cytochrome P450 2D6 inhibitor: SVM model built on 3664 molecules (training set) and tested on 1068 molecules (test set) 10-fold CV: ACC=0.79 / AUC=0.85 External: ACC=0.81 / AUC=0.87	No
CYP3A4 inhibitor? Cytochrome P450 3A4 inhibitor: SVM model built on 7518 molecules (training set) and tested on 2579 molecules (test set) 10-fold CV: ACC=0.77 / AUC=0.85 External: ACC=0.78 / AUC=0.86	No
Log Kp (skin permeation)? Skin permeation: QSPR model implemented from Potts RO and Guy RH. 1992 Pharm. Res.	-7.22 cm/s

Druglikeness

Lipinski? Lipinski (Pfizer) filter: implemented from Lipinski CA. et al. 2001 Adv. Drug Deliv. Rev. MW ≤ 500 MLOGP ≤ 4.15 N or O ≤ 10 NH or OH ≤ 5	0.0
Ghose? Ghose filter: implemented from Ghose AK. et al. 1999 J. Comb. Chem. 160 ≤ MW ≤ 480 -0.4 ≤ WLOGP ≤ 5.6 40 ≤ MR ≤ 130 20 ≤ atoms ≤ 70	None
Veber? Veber (GSK) filter: implemented from Veber DF. et al. 2002 J. Med. Chem. Rotatable bonds ≤ 10 TPSA ≤ 140	0.0
Egan? Egan (Pharmacia) filter: implemented from Egan WJ. et al. 2000 J. Med. Chem. WLOGP ≤ 5.88 TPSA ≤ 131.6	0.0
Muegge? Muegge (Bayer) filter: implemented from Muegge I. et al. 2001 J. Med. Chem. 200 ≤ MW ≤ 600 -2 ≤ XLOGP ≤ 5 TPSA ≤ 150 Num. rings ≤ 7 Num. carbon > 4 Num. heteroatoms > 1 Num. rotatable bonds ≤ 15 H-bond acc. ≤ 10 H-bond don. ≤ 5	2.0
Bioavailability Score? Abbott Bioavailability Score: Probability of F > 10% in rat implemented from Martin YC. 2005 J. Med. Chem.	0.55

Medicinal Chemistry

PAINS? Pan Assay Interference Structures: implemented from Baell JB. & Holloway GA. 2010 J. Med. Chem.	0.0 alert
Brenk? Structural Alert: implemented from Brenk R. et al. 2008 ChemMedChem	1.0 alert: heavy_metal
Leadlikeness? Leadlikeness: implemented from Teague SJ. 1999 Angew. Chem. Int. Ed. 250 ≤ MW ≤ 350 XLOGP ≤ 3.5 Num. rotatable bonds ≤ 7	No; 1 violation:MW<1.0
Synthetic accessibility? Synthetic accessibility score: from 1 (very easy) to 10 (very difficult) based on 1024 fragmental contributions (FP2) modulated by size and complexity penaties, trained on 12’782’590 molecules and tested on 40 external molecules (r² = 0.94)	2.08

Application In Synthesis of [ 1003845-06-4 ]

* All experimental methods are cited from the reference, please refer to the original source for details. We do not guarantee the accuracy of the content in the reference.

Upstream synthesis route of [ 1003845-06-4 ]
Downstream synthetic route of [ 1003845-06-4 ]

[ 1003845-06-4 ] Synthesis Path-Upstream 1~2

1
[ 110-91-8 ]
[ 1003845-06-4 ]
[ 870521-33-8 ]

Yield	Reaction Conditions	Operation in experiment
70%	With triethylamine In ethanol at 20℃; for 1 h;	2-Chloropyrimidin-5-ylboronic acid (1 g, 6.32 mmol), morpholine (2.19 mL,25.26 mmol) and triethylamine (0.88 mL, 6.32 mmol) were stirred in ethanol (25 mL) at20°C for 1 h. Water (50 mL) was slowly added to the reaction mixture. The resultingprecipitate was filtered and washed with water to afford the title compound (950 mg,70percent) as a cream solid. H (250 MHz, DMSO-d6) 8.63 (s, 2H), 8.05 (s, 2H), 3.68 (ddd, J23.4, 5.7, 3.9 Hz, 8H).
70%	With triethylamine In ethanol at 20℃; for 1 h;	A solution of (2-chloropyrimidin-5-yl)boronic acid (1 g, 6.32 mmol), morpholine (2.19 mL, 25.26 mmol) and triethylamine (0.9 mL, 6.32 mmol) in ethanol (25 mL) was stirred at 20°C for 1 h. Water (50 mL) was slowly added to the reaction mixture to form a precipitate that was collected by filtration, to afford the title compound (950 mg, 70percent) ascream solid. H (250 MHz, DMSO-d6) 8.63 (s, 2H), 8.05 (s, 2H), 3.68 (ddd, J23.4, 5.7,3.9 Hz, 8H). LCMS m/z 210 [M+H].
70%	With triethylamine In ethanol at 20℃; for 1 h; Inert atmosphere	A solution of (2-chloropyrimidin-5-yl)boronic acid (1 g, 6.32 mmol), morpholine (2.19 mL, 25.26 mmol) and triethylamine (0.9 mL, 6.32 mmol) in ethanol (25 mL) was stirred at 20°C for 1 h. Water (50 mL) was slowly added to the reaction mixture to form a precipitate that was collected by filtration, to afford the title compound as a cream solid (950 mg, 70percent). δΗ (250 MHz, DMSO-d₆) 8.63 (s, 2H), 8.05 (s, 2H), 3.68 (ddd, J23.4, 5.7, 3.9 Hz, 8H). LCMS(ES⁺) 210 (M+H)⁺.

70%	With triethylamine In ethanol at 20℃; for 1 h;	A solution of (2-chloropyrimidin-5-yl)boronic acid (1 g, 6.32 mmol), morpholine (2.19 mL, 25.26 mmol) and triethylamine (0.9 mL, 6.32 mmol) in ethanol (25 mL) was stirred at 20°C for 1 h. Water (50 mL) was slowly added to the reaction mixture to form a precipitate that was collected by filtration, to afford the title compound as a cream solid (950 mg, 70percent). δΗ (250 MHz, DMSO-d₆) 8.63 (s, 2H), 8.05 (s, 2H), 3.68 (ddd, J23.4, 5.7, 3.9 Hz, 8H). LCMS(ES⁺) 210.0 (M+H)⁺.
70%	With triethylamine In ethanol at 20℃; for 1 h;	A solution of(2-chloropyrimidin-5-yl)boronic acid (1 g, 6.32 mmol), morpholine (2.19 mL, 25.26 mmol) and triethylamine (0.9 mL, 6.32 mmol) in ethanol (25 mL) was stirred at 20°C for 1 h. Water (50 mL) was slowly added to the reaction mixture to form a precipitate that was collected by filtration, to afford the title compound as a cream solid(950 mg, 70percent). oH (250 MHz, DMSO-d6) 8.63 (s, 2H), 8.05 (s, 2H), 3.68 (ddd, J23.4, 5.7, 3.9 Hz, 8H). LCMS(ES) 210 (M+H).
68%	With triethylamine In ethanol at 80℃; for 5 h;	A mixture of 2-chloropyrimidin-5-ylboronic acid (3 g, 19.0 mmol), morpholine (1.66 mL, 19 mmol) and triethylamine (1.67 mL, 19.19 mmol) in EtOH (20 mL) was stirred at 80°C for 5 h. LCMS indicated completion of the reaction. The reaction mixturewas concentrated in vacuo and the residue was taken up in ethanol (approximately 5 mL). Diethyl ether was added, and the triethylamine hydrochloride salt that crystallised out was filtered and discarded. The filtrate was concentrated in vacuo and water (approximately 10 mL) was added. The mixture was placed in a refrigerator for 1 h, after which time the resulting solid was filtered off, washed with the minimum amount of water and dried bysuction, to give the title compound (2.7 g, 68percent) as an off-white solid. oH (DMSO-d6)8.64 (s, 2H), 8.08 (s, 2H), 3.73 (m, 4H), 3.65 (m, 4H). LCMS (ES+) 210 (M+H), RT0.15 minutes.
68%	With triethylamine In ethanol at 80℃; for 5 h;	A mixture of 2-chloropyrimidin-5-ylboronic acid (3 g, 19.0 mmol), morpholine (1.66 mL, 19.0 mmol) and triethylamine (1.67 mL, 19.2 mmol) in EtOH (20 mL) wasstirred at 80°C for 5 h. The reaction mixture was concentrated in vacuo and the residue was taken up in Et20 (approximately 5 mL). Et20 was added, and the triethylamine hydrochloride salt that crystallised out was filtered and discarded. The filtrate was concentrated in vacuo and water (approximately 10 mL) was added. The mixture was placed in a refrigerator for 1 h, after which time the resulting solid was filtered off, washed with the minimum amount of water and dried by suction, to give the title compound (2.7 g, 68percent) as an off-white solid. oH (DMSO-d6) 8.64 (s, 2H), 8.08 (s, 2H), 3.73 (m, 4H), 3.65 (m, 4H). LCMS (ESj 210 (M+H), RT 0.15 minutes.
68%	With triethylamine In ethanol at 80℃; for 5 h;	INTERMEDIATE 4 2-(Morpholin-4-yl)pyrimidin-5 -ylboronic acidA mixture of 2-chloropyrimidin-5-ylboronic acid (3.0 g, 19.0 mmol), morpholine (1.66 mL, 19.0 mmol) and triethylamine (1.67 mL, 19.2 mmol) in EtOH (20 mL) was stirred at 80°C for 5 h. The reaction mixture was concentrated in vacuo and the residue was taken up in Et20 (approximately 5 mL). Et20 was added, and the triethylamine hydrochloride salt that crystallised out was filtered and discarded. The filtrate was concentrated in vacuo and water (approximately 10 mL) was added. The mixture was placed in a refrigerator for 1 h, after which time the resulting solid was filtered off,washed with the minimum amount of water and dried by suction, to give the title compound (2.7 g, 68percent) as an off-white solid. H (400 MHz, DMSO-d6) 8.64 (s, 2H), 8.08 (s, 2H), 3.73 (m, 4H), 3.65 (m, 4H). LCMS (ESj 210 (M+H), RT 0.15 minutes.
68%	With triethylamine In ethanol at 80℃; for 5 h;	INTERMEDIATE 5 2- (Morpholin-4- yl)p yrimidin- 5 – ylboronic acid A mixture of 2-chloropyrimidin-5-ylboronic acid (3 g, 19.0 mmol), morpholine (1.66 mL, 19.0 mmol) and triethylamine (1.67 mL, 19.2 mmol) in EtOH (20 mL) was stirred at 80°C for 5 h. The reaction mixture was concentrated in vacuo and the residue was taken up in Et₂0 (approximately 5 mL). Et₂0 was added, and the triethylamine hydrochloride salt that crystallised out was filtered and discarded. The filtrate was concentrated in vacuo and water (approximately 10 mL) was added. The mixture was placed in a refrigerator for 1 h, after which time the resulting solid was filtered off, washed with the minimum amount of water and dried by suction, to give the title compound (2.7 g, 68percent) as an off-white solid. δ_Η (DMSO-d₆) 8.64 (s, 2H), 8.08 (s, 2H), 3.73 (m, 4H), 3.65 (m, 4H). LCMS (ES⁺) 210 (M+H)⁺, RT 0.15 minutes.
68%	With triethylamine In ethanol at 80℃; for 5 h;	INTERMEDIATE 3 2-(Morpholin-4-yl)pyrimidin-5 -ylboronic acid A mixture of 2-chloropyrimidin-5 -ylboronic acid (3.0 g, 19.0 mmol), morpholine (1.66 mL, 19.0 mmol) and triethylamine (1.67 mL, 19.2 mmol) in EtOH (20 mL) was stirred at 80°C for 5 h. The reaction mixture was concentrated in vacuo and the residue was taken up in Et₂0 (approximately 5 mL). Et₂0 was added, and the triethylamine hydrochloride salt that crystallised out was filtered and discarded. The filtrate was concentrated in vacuo and water (approximately 10 mL) was added. The mixture was placed in a refrigerator for 1 h, after which time the resulting solid was filtered off, washed with the minimum amount of water and dried by suction, to give the title compound (2.7 g, 68percent) as an off-white solid. δ_Η (400 MHz, DMSO-dg) 8.64 (s, 2H), 8.08 (s, 2H), 3.73 (m, 4H), 3.65 (m, 4H). LCMS (ES⁺) 210 (M+H)⁺, RT 0.15 minutes.

References:

[1] Patent: WO2015/86506, 2015, A1, . Location in patent: Page/Page column 131.

[2] Patent: WO2015/86512, 2015, A1, . Location in patent: Page/Page column 102.

[3] Patent: WO2015/86527, 2015, A1, . Location in patent: Page/Page column 114; 115.

[4] Patent: WO2015/86526, 2015, A1, . Location in patent: Page/Page column 147.

[5] Patent: WO2015/86525, 2015, A1, . Location in patent: Page/Page column 121; 122.

[6] Patent: WO2014/9295, 2014, A1, . Location in patent: Page/Page column 128; 129.

[7] Patent: WO2015/86502, 2015, A1, . Location in patent: Page/Page column 82; 83.

[8] Patent: WO2015/86511, 2015, A1, . Location in patent: Page/Page column 74; 75.

[9] Patent: WO2015/86501, 2015, A1, . Location in patent: Page/Page column 89.

[10] Patent: WO2015/86496, 2015, A1, . Location in patent: Page/Page column 74.

2
[ 76-09-5 ]
[ 1003845-06-4 ]
[ 1003845-08-6 ]

Yield	Reaction Conditions	Operation in experiment
100%	With magnesium sulfate In toluene at 20℃; for 15 h;	34). Synthesis of 2-chloro-5-(4,4,5,5-tetramethyl-[1,3,2]dioxaborolan-2-yl)-pyrimidine; To a solution of 5-bromo-2-chloro-pyrimidine (10 mmol, 1.93 g) and triisopropyl borate (12 mmol, 2.8 ml.) in toluene (16 ml) and THF (4 mi_) is added n-buty. lithium \r, hexane (1.58 M, 12 mmol, 7.6 mL) dropwise at -78 ⁰C over 45 min and stirred at -78 ⁰C for 1 hour. The mixture is warmed to -20 ⁰C, then added aq. hydrogen chloride (1M, 20 mL). The mixture is warmed to room temperature. The precipitate is collected and washed with hexane to give a colorless powder (808 mg, 51percent). A mixture of the powder (3.63 mmol, 575 mg), pinacol (3.81 mmol, 450 mg) and MgSO₄ (18.15 mmol, 2.2 g) in toluene (10 mL) is <n=”192″/>stirred at room temperature for 15 hour. The mixture is filtrated and the solution is concentrated under reduced pressure. The resultant solid is washed with water to give 2- chloro-5-(4,4,5,5-tetramethyl-[1 ,3,2]dioxaborolan-2-yl)-pyrimidine (875 mg, quant); ESI-MS m/z: 159 [M+1-pinacol]\ Retention time 1.75 min (condition A).
100%	With magnesium sulfate In toluene at 20℃; for 15 h;	Example 14; 1) Synthesis of 2-chloro-5-(4,4,5,5-tetramethyl-[1,3,2]dioxaborolan-2-yl)-pyrimidine To a solution of 5-bromo-2-chloro-pyrimidine (10 mmol, 1.93 g) and triisopropyl borate (12 mmol, 2.8 mL) in toluene (16 mL) and THF (4 mL) is added n-butyl lithium in hexane (1.58 M, 12 mmol, 7.6 mL) dropwise at -78° C. over 45 min and stirred at -78° C. for 1 hour. The mixture is warmed to -20° C., then added aqueous 1 M HCl (20 mL). The mixture is warmed to room temperature. The precipitate is collected and washed with hexane to give a colorless powder (808 mg, 51percent). A mixture of the powder (3.63 mmol, 575 mg), pinacol (3.81 mmol, 450 mg) and MgSO4 (18.15 mmol, 2.2 g) in toluene (10 mL) is stirred at room temperature for 15 hour. The mixture is filtrated and the solution is concentrated under reduced pressure. The resultant solid is washed with water to give 2-chloro-5-(4,4,5,5-tetramethyl-[1,3,2]dioxaborolan-2-yl)-pyrimidine (875 mg, quant); ESI-MS m/z: 159 [M+1-pinacol]+, Retention time 1.75 min (condition A).

References:

[1] Patent: WO2008/9435, 2008, A1, . Location in patent: Page/Page column 189-190.

[2] Patent: US2009/118287, 2009, A1, . Location in patent: Page/Page column 67-68.

Yield	Reaction Conditions	Operation in experiment
	With sodium perborate tetrahydrate; In tetrahydrofuran; water; at 20℃; for 18h;	A 2.0 L round bottom flask was charged with (2-chloropyrimidin-5-yl)boronic acid (40.0 g, 253 mmol), THF (440 mL) and water (440 mL). Solid sodium perborate tetrahydrate (1 17 g, 758 mmol) was added in one portion and the resulting suspension stirred at r.t. for 18 hours. Note: after 10 minutes of solid sodium perborate tetrahydrate addition a small exotherm occurred, from 28°C to 34°C over 30min. The reaction was quenched with saturated NH4CI (250 mL) and EtOAc (250 mL) was added. A 10percent solution of sodium bisulfite (1 L) was added to the mixture portionwise at 0°C until no more peroxide was detected by I-starch paper. (Note: Exotherm occurred during sodium bisulfite addition). The aqueous phase was separated and extracted-with further portions of EtOAc (2 x250 mL). Solid NaCl was added to the aqueous phase until no-more dissolved then extracted with THF (2 x 250 mL). All the organic phases were combined and dried-over MgS04, filtered and concentrated to obtain a yellow solid. The product-solid was suspended in toluene heptane (1 :1 ratio^ 800 mL) and the mixture heated to 50°C The mixture was cooled to r.t. and the solid collected by filtration and washed with toluene/heptane (1 : 1 ratio, 250 mL) followed by heptane (150 mL). The product solid was suspended in 15percent toluene/DCM (100 mL) at r.t., filtered and washed twice with toluene/DCM (1 : 1 ratio, x50 mL) then with 100percent DCM (100 mL) to give 2-chloropyrimidin-5-ol.

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